Figure 1. Length Frequencies with age modes (red) and total distributions (green) from the statistical estimation overlayed.

Figure 2. Deterministic numbers-at-age from age slicing procedure.

Figure 3. Statistical estimates of numbers-at-age from the mixture distribution analysis.

Figure 4. A comparison of catch numbers-at-age from the statistical and deterministic ageing procedures.

Figure 5. Standardised residuals of the proportion of numbers-at-age from the deterministic age slicing procedure (red negative and black positive residuals).

Figure 6. Standardised residuals for the proportion of numbers-at-age from the statistical mixture distribution analysis (red negative and black positive residuals).

Figure 7. Comparison of total catch biomass derived from different procedures.

[1] 1.018553

Figure 8. Catch-at-size by lustrum (5 year block).

Figure 9. Powell-Wheatherall plots

Figure 10. Estimates of Z derived from the Powell-Wetherall plots; showing the estimates from each year (black line with points) and a smoother (blue continuous line).

Figure 11. Catch curves by lustrum from statisical age estimates.

Figure 12. Estimated selectivity by lustrum.

Selectivity by gear

Figure 13. Catch curves by gear based on age estimates

Selectivity by gear and lustrum

Figure 14. Catch curves by gear and lustrum based on statistical age estimates.

XSA Continuity Run

Figure 15. XSA diagnostics from continuity run; residuals against fitted value.

Figure 16. XSA diagnostics from continuity run; residuals against year.

Figure 17. XSA diagnostics from continuity run; Calibration regression plots for age 2 (outlier for Scilian gillnet removed).

Figure 18. XSA diagnostics from continuity run; Calibration regression plots for age 3 (outlier for Scilian gillnet removed).

Figure 19. XSA diagnostics from continuity run; Calibration regression plots for age 4 (outlier for Scilian gillnet removed).

Figure 20. XSA diagnostics from continuity run; AR plots of lagged residuals

Figure 21. XSA diagnostics from continuity run; QQ plots to check for normality

Figure 22. XSA diagnostics from continuity run; weights for terminal year Ns for each CPUE observation and shrinkage

Figure 23. XSA time series estimates by CPUE series.

Figure 24. Retrospective XSA time series estimates.

Alternative Run

Figure 25. XSA diagnostics from alternative run; residuals against fitted value.

Figure 26. XSA diagnostics from from alternative run; residuals against year.

Figure 27. XSA diagnostics from from alternative run; Calibration regression plots for age 2.

Figure 28. XSA diagnostics from alternative run; Calibration regression plots for age 3.

Figure 29. XSA diagnostics from alternative run; Calibration regression plots for age 4.

Figure 30. XSA diagnostics alternative run; AR plots of lagged residuals

Figure 31. XSA diagnostics alternative run; QQ plots to check for normality

Figure 32. XSA diagnostics alternative run; weights for terminal year Ns for each CPUE observation and shrinkage

Figure 33. XSA time series estimates by CPUE series.

Figure 34. Retrospective XSA time series estimates.

Stock Status

Figure 35. XSA alternative run.

Stock Status

Figure 36. Stock Recruitment Relationship

[1] TRUE

Figure 37a. Equilibrium Analysis with reference points.

Figure 37b. Equilibrium Analysis with observations.

Figure 38. Kobe Phase Plot.

Figure 39. Current and mesopelagic selection patterns.

Figure 40. Projections for current selection pattern.

Figure 41. Projections for 50:50 current:mesopelagic selection pattern.

Tables

Table 1a. XSA Control options from continuity run.

tol          1e-09 
maxit        30 
min.nse          0.3 
fse          0.3 
rage         1 
qage         6 
shk.n        TRUE 
shk.f        TRUE 
shk.yrs          5 
shk.ages         5 
window       100 
tsrange          20 
tspower          3 
vpa          TRUE 

Table 1b. XSA Control options from alternative run.

tol          1e-09 
maxit        30 
min.nse          0.3 
fse          0.5 
rage         1 
qage         6 
shk.n        TRUE 
shk.f        TRUE 
shk.yrs          5 
shk.ages         1 
window       100 
tsrange          20 
tspower          3 
vpa          TRUE 

Table 2a. Reference Points

An object of class "FLPar"
        quantity
refpt    harvest    yield      rec        ssb        biomass   
  virgin 0.0000e+00 0.0000e+00 8.8399e+02 2.4321e+05 2.7406e+05
  msy    2.4296e-01 1.5835e+04 8.8385e+02 4.9748e+04 7.3242e+04
  crash  3.0843e+00 2.1509e-03 2.7182e-04 3.0748e-06 1.5639e-03
  f0.1   1.4898e-01 1.4890e+04 8.8392e+02 8.4950e+04 1.1095e+05
  fmax   2.4308e-01 1.5835e+04 8.8385e+02 4.9715e+04 7.3206e+04
  spr.30 1.7428e-01 1.5391e+04 8.8391e+02 7.3029e+04 9.8316e+04
units:  NA 

Table 2b. Reference Points with 50% Mesopelagic selection pattern.

An object of class "FLPar"
        quantity
refpt    harvest    yield      rec        ssb        biomass   
  virgin 0.0000e+00 0.0000e+00 8.8399e+02 2.4321e+05 2.7406e+05
  msy    2.4180e-01 1.7045e+04 8.8385e+02 4.8891e+04 7.3793e+04
  crash  3.6569e+00 2.4233e-03 2.7950e-04 3.1616e-06 1.9020e-03
  f0.1   1.4108e-01 1.5917e+04 8.8392e+02 8.6050e+04 1.1319e+05
  fmax   2.4193e-01 1.7045e+04 8.8385e+02 4.8858e+04 7.3757e+04
  spr.30 1.6864e-01 1.6532e+04 8.8391e+02 7.2957e+04 9.9457e+04
units:  NA 

Table 3. Stock information

An object of class "FLStock"
Slot "catch":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985  1986  1987  1988  1989  1990  1991  1992  1993  1994  1995 
  all 15292 16765 18320 20365 17762 16018 15746 14709 13265 16082 13015
     year
age   1996  1997  1998  1999  2000  2001  2002  2003  2004  2005  2006 
  all 12053 14693 14369 13699 15569 15006 12814 15674 14405 14601 14893
     year
age   2007  2008  2009  2010  2011  2012  2013 
  all 14227 12164 11840 13430 11423  9888 11254

units:  NA 

Slot "catch.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0  21.4729  20.6035  44.3813  63.1249  74.3797  15.3243  27.4159
  1 134.5648  90.5752 153.1706 265.5847 197.1327 234.2886 174.9776
  2 134.6194 177.6181 133.4858 168.8764 176.0136 289.0440 196.6749
  3  79.1531  76.0513  81.8548  87.5656  86.8658  74.0081  92.0008
  4  42.6496  45.2544  59.8951  65.5141  54.4569  24.5272  36.7259
  5  51.0371  58.7734  65.9006  59.3421  45.0798  24.1648  32.4736
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0  56.2606  47.2734  67.7528  53.5708  27.6208  26.5902  46.3369
  1 172.1673 239.6096 190.6157 246.8151 176.5885 156.1288 248.9399
  2 219.3156 198.0215 251.2519 164.9636 162.4746 195.0504 160.8919
  3  64.1896  49.8246  69.1512  57.0136  68.1938  87.2302  55.0914
  4  30.4537  23.7044  26.3690  23.1110  23.1912  40.6634  32.5162
  5  33.1255  27.0431  35.9536  26.2792  21.6804  24.0022  38.8505
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0  31.6699  10.2255  20.6051   9.1971  56.6800  60.4517  14.2259
  1 177.5012 208.9787 193.4171 288.4701 203.1130 245.1487 221.9711
  2 155.8745 184.8450 200.5366 215.1277 270.0108 174.7456 207.5041
  3  66.5933  75.2087  81.1425  46.1867  77.5790  66.1635  64.2196
  4  35.2808  38.1185  29.4873  17.7672  30.3505  31.7959  28.6761
  5  33.5977  36.8194  29.8884  20.7071  21.6038  31.4460  29.8566
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0  27.1267  24.4187   9.5989  12.7435  26.3902  87.4014  21.9434
  1 161.6561 267.5342 274.0811 182.0861 151.5678 123.6516 113.8618
  2 200.6652 160.1002 184.8834 153.2820 138.1137 131.1289  95.5075
  3  60.1729  68.8383  58.8265  57.7290  78.5488  75.0686  42.5593
  4  31.3468  31.1331  21.6520  32.8373  42.3556  23.5957  20.2280
  5  39.2381  28.2827  14.0846  20.9188  28.7229  22.5787  26.3230
   year
age 2013    
  0   3.1197
  1 128.6195
  2 159.9425
  3  51.9627
  4  25.0570
  5  25.7617

units:  NA 

Slot "catch.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0   3.5973   3.3550   3.8595   4.1875   3.3635   3.5320   3.6676
  1  10.7577  10.7182   9.9559  10.2292  10.6368  10.7895  10.9384
  2  22.8482  23.3794  23.3902  22.3407  22.6277  22.5130  22.9624
  3  39.9227  39.9683  40.8690  41.1086  40.7663  39.8577  39.8578
  4  60.2237  61.2643  62.0729  60.7125  59.9180  59.6007  59.5622
  5  92.5657  94.9294  95.9938  95.6335  95.8431  93.1051  96.6367
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0   3.5290   3.7548   3.6669   3.4276   3.7449   3.6454   3.4840
  1  11.7756  11.0303  11.7135  10.3914  10.4839  10.7970   9.8658
  2  21.0501  21.0571  21.5953  22.7362  22.7384  23.3870  22.5815
  3  39.8598  39.8651  39.8655  39.8577  39.8577  39.8577  40.4127
  4  59.8357  59.9089  59.7883  59.7285  59.5101  59.6189  59.9181
  5  97.3624  97.3884  98.8695  98.1105  97.6339  91.9874  96.0047
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0   4.1242   3.7035   3.7259   3.6340   3.2894   3.4900   3.4467
  1  11.1596  10.7847  10.9189  10.3710  11.6721   9.9678  11.4007
  2  21.9276  22.7796  22.7163  21.7204  21.7040  22.5322  21.5889
  3  39.8610  39.9498  39.8579  39.8577  39.8586  39.8591  39.8795
  4  59.8914  59.9181  59.4784  59.7334  59.5068  59.8700  59.7541
  5  94.9498  95.6923 101.7694 101.2668  98.2296  97.4292 101.0340
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0   3.3710   3.4884   3.5483   4.1936   4.0896   3.5494   3.6247
  1  11.7997  10.4942  10.9215  10.5780  10.4251  10.6537  11.3421
  2  21.7698  22.7073  21.6111  22.0457  22.7801  22.3551  21.9654
  3  39.8665  40.1303  39.8578  39.8599  39.8629  39.9490  40.2181
  4  60.0432  59.5603  59.4830  60.3255  59.6308  58.8395  59.6101
  5 100.9875 101.1686  95.5016  94.6294  95.1012  99.6323  99.8336
   year
age 2013    
  0   3.6779
  1  11.3741
  2  22.2070
  3  39.8856
  4  59.4617
  5  99.6322

units:  NA 

Slot "discards":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997
  all 0    0    0    0    0    0    0    0    0    0    0    0    0   
     year
age   1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
  all 0    0    0    0    0    0    0    0    0    0    0    0    0   
     year
age   2011 2012 2013
  all 0    0    0   

units:  NA 

Slot "discards.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  1 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  2 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  3 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  4 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  5 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  1 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  2 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  3 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  4 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
  5 0    0    0    0    0    0    0    0    0    0    0    0    0    0   
   year
age 2013
  0 0   
  1 0   
  2 0   
  3 0   
  4 0   
  5 0   

units:  NA 

Slot "discards.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985    1986    1987    1988    1989    1990    1991    1992   
  0  3.5973  3.3550  3.8595  4.1875  3.3635  3.5320  3.6676  3.5290
  1 10.7577 10.7182  9.9559 10.2292 10.6368 10.7895 10.9384 11.7756
  2 22.8482 23.3794 23.3902 22.3407 22.6277 22.5130 22.9624 21.0501
  3 39.9227 39.9683 40.8690 41.1086 40.7663 39.8577 39.8578 39.8598
  4 60.2237 61.2643 62.0729 60.7125 59.9180 59.6007 59.5622 59.8357
  5  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
   year
age 1993    1994    1995    1996    1997    1998    1999    2000   
  0  3.7548  3.6669  3.4276  3.7449  3.6454  3.4840  4.1242  3.7035
  1 11.0303 11.7135 10.3914 10.4839 10.7970  9.8658 11.1596 10.7847
  2 21.0571 21.5953 22.7362 22.7384 23.3870 22.5815 21.9276 22.7796
  3 39.8651 39.8655 39.8577 39.8577 39.8577 40.4127 39.8610 39.9498
  4 59.9089 59.7883 59.7285 59.5101 59.6189 59.9181 59.8914 59.9181
  5  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
   year
age 2001    2002    2003    2004    2005    2006    2007    2008   
  0  3.7259  3.6340  3.2894  3.4900  3.4467  3.3710  3.4884  3.5483
  1 10.9189 10.3710 11.6721  9.9678 11.4007 11.7997 10.4942 10.9215
  2 22.7163 21.7204 21.7040 22.5322 21.5889 21.7698 22.7073 21.6111
  3 39.8579 39.8577 39.8586 39.8591 39.8795 39.8665 40.1303 39.8578
  4 59.4784 59.7334 59.5068 59.8700 59.7541 60.0432 59.5603 59.4830
  5  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000
   year
age 2009    2010    2011    2012    2013   
  0  4.1936  4.0896  3.5494  3.6247  3.6779
  1 10.5780 10.4251 10.6537 11.3421 11.3741
  2 22.0457 22.7801 22.3551 21.9654 22.2070
  3 39.8599 39.8629 39.9490 40.2181 39.8856
  4 60.3255 59.6308 58.8395 59.6101 59.4617
  5  0.0000  0.0000  0.0000  0.0000  0.0000

units:  NA 

Slot "landings":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985  1986  1987  1988  1989  1990  1991  1992  1993  1994  1995 
  all 15292 16765 18320 20365 17762 16018 15746 14709 13265 16082 13015
     year
age   1996  1997  1998  1999  2000  2001  2002  2003  2004  2005  2006 
  all 12053 14693 14369 13699 15569 15006 12814 15674 14405 14601 14893
     year
age   2007  2008  2009  2010  2011  2012  2013 
  all 14227 12164 11840 13430 11423  9888 11254

units:  NA 

Slot "landings.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0  21.4729  20.6035  44.3813  63.1249  74.3797  15.3243  27.4159
  1 134.5648  90.5752 153.1706 265.5847 197.1327 234.2886 174.9776
  2 134.6194 177.6181 133.4858 168.8764 176.0136 289.0440 196.6749
  3  79.1531  76.0513  81.8548  87.5656  86.8658  74.0081  92.0008
  4  42.6496  45.2544  59.8951  65.5141  54.4569  24.5272  36.7259
  5  51.0371  58.7734  65.9006  59.3421  45.0798  24.1648  32.4736
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0  56.2606  47.2734  67.7528  53.5708  27.6208  26.5902  46.3369
  1 172.1673 239.6096 190.6157 246.8151 176.5885 156.1288 248.9399
  2 219.3156 198.0215 251.2519 164.9636 162.4746 195.0504 160.8919
  3  64.1896  49.8246  69.1512  57.0136  68.1938  87.2302  55.0914
  4  30.4537  23.7044  26.3690  23.1110  23.1912  40.6634  32.5162
  5  33.1255  27.0431  35.9536  26.2792  21.6804  24.0022  38.8505
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0  31.6699  10.2255  20.6051   9.1971  56.6800  60.4517  14.2259
  1 177.5012 208.9787 193.4171 288.4701 203.1130 245.1487 221.9711
  2 155.8745 184.8450 200.5366 215.1277 270.0108 174.7456 207.5041
  3  66.5933  75.2087  81.1425  46.1867  77.5790  66.1635  64.2196
  4  35.2808  38.1185  29.4873  17.7672  30.3505  31.7959  28.6761
  5  33.5977  36.8194  29.8884  20.7071  21.6038  31.4460  29.8566
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0  27.1267  24.4187   9.5989  12.7435  26.3902  87.4014  21.9434
  1 161.6561 267.5342 274.0811 182.0861 151.5678 123.6516 113.8618
  2 200.6652 160.1002 184.8834 153.2820 138.1137 131.1289  95.5075
  3  60.1729  68.8383  58.8265  57.7290  78.5488  75.0686  42.5593
  4  31.3468  31.1331  21.6520  32.8373  42.3556  23.5957  20.2280
  5  39.2381  28.2827  14.0846  20.9188  28.7229  22.5787  26.3230
   year
age 2013    
  0   3.1197
  1 128.6195
  2 159.9425
  3  51.9627
  4  25.0570
  5  25.7617

units:  NA 

Slot "landings.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0   3.5973   3.3550   3.8595   4.1875   3.3635   3.5320   3.6676
  1  10.7577  10.7182   9.9559  10.2292  10.6368  10.7895  10.9384
  2  22.8482  23.3794  23.3902  22.3407  22.6277  22.5130  22.9624
  3  39.9227  39.9683  40.8690  41.1086  40.7663  39.8577  39.8578
  4  60.2237  61.2643  62.0729  60.7125  59.9180  59.6007  59.5622
  5  92.5657  94.9294  95.9938  95.6335  95.8431  93.1051  96.6367
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0   3.5290   3.7548   3.6669   3.4276   3.7449   3.6454   3.4840
  1  11.7756  11.0303  11.7135  10.3914  10.4839  10.7970   9.8658
  2  21.0501  21.0571  21.5953  22.7362  22.7384  23.3870  22.5815
  3  39.8598  39.8651  39.8655  39.8577  39.8577  39.8577  40.4127
  4  59.8357  59.9089  59.7883  59.7285  59.5101  59.6189  59.9181
  5  97.3624  97.3884  98.8695  98.1105  97.6339  91.9874  96.0047
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0   4.1242   3.7035   3.7259   3.6340   3.2894   3.4900   3.4467
  1  11.1596  10.7847  10.9189  10.3710  11.6721   9.9678  11.4007
  2  21.9276  22.7796  22.7163  21.7204  21.7040  22.5322  21.5889
  3  39.8610  39.9498  39.8579  39.8577  39.8586  39.8591  39.8795
  4  59.8914  59.9181  59.4784  59.7334  59.5068  59.8700  59.7541
  5  94.9498  95.6923 101.7694 101.2668  98.2296  97.4292 101.0340
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0   3.3710   3.4884   3.5483   4.1936   4.0896   3.5494   3.6247
  1  11.7997  10.4942  10.9215  10.5780  10.4251  10.6537  11.3421
  2  21.7698  22.7073  21.6111  22.0457  22.7801  22.3551  21.9654
  3  39.8665  40.1303  39.8578  39.8599  39.8629  39.9490  40.2181
  4  60.0432  59.5603  59.4830  60.3255  59.6308  58.8395  59.6101
  5 100.9875 101.1686  95.5016  94.6294  95.1012  99.6323  99.8336
   year
age 2013    
  0   3.6779
  1  11.3741
  2  22.2070
  3  39.8856
  4  59.4617
  5  99.6322

units:  NA 

Slot "stock":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

     year
age   1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997
  all NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA  
     year
age   1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010
  all NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA   NA  
     year
age   2011 2012 2013
  all NA   NA   NA  

units:  NA * NA 

Slot "stock.n":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0  765.366  800.120  999.174 1133.759  970.817  827.703  843.546
  1  820.176  607.241  636.480  777.997  871.280  727.747  663.828
  2  567.780  550.348  415.591  383.445  398.911  536.111  385.708
  3  336.816  343.860  291.294  220.539  163.026  169.315  181.574
  4  181.484  204.613  213.146  165.000  102.201   56.112   72.480
  5  217.175  265.738  234.518  149.455   84.603   55.283   64.088
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0 1036.831  900.886 1032.823  903.839  809.627  916.908  894.445
  1  665.887  798.116  694.922  784.477  691.663  637.932  726.694
  2  386.326  390.517  438.423  397.784  420.876  407.636  381.989
  3  140.475  121.260  143.192  135.565  178.138  199.140  159.672
  4   66.641   57.682   54.712   55.532   60.009   84.795   85.085
  5   72.487   65.806   74.599   63.145   56.100   50.052  101.659
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0  889.401  923.087 1126.060  865.697 1032.159 1003.277  788.406
  1  690.493  699.590  746.525  903.333  700.466  793.912  766.868
  2  371.835  405.865  385.236  437.450  480.855  391.175  430.061
  3  168.878  165.042  167.197  136.720  166.258  153.506  164.143
  4   81.352   78.668   67.951   64.492   70.533   66.856   66.536
  5   77.471   75.987   68.876   75.163   50.206   66.120   69.275
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0  987.260  941.323  784.538  702.436  661.855  872.543  762.029
  1  632.646  783.808  748.643  633.656  563.598  518.060  635.579
  2  428.611  372.733  401.921  367.438  355.339  325.311  313.015
  3  166.945  171.768  162.047  163.959  163.751  167.300  149.020
  4   76.910   82.776   79.037   79.976   82.508   63.971   69.909
  5   96.272   75.198   51.414   50.948   55.952   61.214   90.974
   year
age 2013    
  0  679.782
  1  604.085
  2  417.887
  3  170.581
  4   83.801
  5   86.158

units:  NA 

Slot "stock.wt":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985     1986     1987     1988     1989     1990     1991    
  0   3.5973   3.3550   3.8595   4.1875   3.3635   3.5320   3.6676
  1  10.7577  10.7182   9.9559  10.2292  10.6368  10.7895  10.9384
  2  22.8482  23.3794  23.3902  22.3407  22.6277  22.5130  22.9624
  3  39.9227  39.9683  40.8690  41.1086  40.7663  39.8577  39.8578
  4  60.2237  61.2643  62.0729  60.7125  59.9180  59.6007  59.5622
  5  92.5657  94.9294  95.9938  95.6335  95.8431  93.1051  96.6367
   year
age 1992     1993     1994     1995     1996     1997     1998    
  0   3.5290   3.7548   3.6669   3.4276   3.7449   3.6454   3.4840
  1  11.7756  11.0303  11.7135  10.3914  10.4839  10.7970   9.8658
  2  21.0501  21.0571  21.5953  22.7362  22.7384  23.3870  22.5815
  3  39.8598  39.8651  39.8655  39.8577  39.8577  39.8577  40.4127
  4  59.8357  59.9089  59.7883  59.7285  59.5101  59.6189  59.9181
  5  97.3624  97.3884  98.8695  98.1105  97.6339  91.9874  96.0047
   year
age 1999     2000     2001     2002     2003     2004     2005    
  0   4.1242   3.7035   3.7259   3.6340   3.2894   3.4900   3.4467
  1  11.1596  10.7847  10.9189  10.3710  11.6721   9.9678  11.4007
  2  21.9276  22.7796  22.7163  21.7204  21.7040  22.5322  21.5889
  3  39.8610  39.9498  39.8579  39.8577  39.8586  39.8591  39.8795
  4  59.8914  59.9181  59.4784  59.7334  59.5068  59.8700  59.7541
  5  94.9498  95.6923 101.7694 101.2668  98.2296  97.4292 101.0340
   year
age 2006     2007     2008     2009     2010     2011     2012    
  0   3.3710   3.4884   3.5483   4.1936   4.0896   3.5494   3.6247
  1  11.7997  10.4942  10.9215  10.5780  10.4251  10.6537  11.3421
  2  21.7698  22.7073  21.6111  22.0457  22.7801  22.3551  21.9654
  3  39.8665  40.1303  39.8578  39.8599  39.8629  39.9490  40.2181
  4  60.0432  59.5603  59.4830  60.3255  59.6308  58.8395  59.6101
  5 100.9875 101.1686  95.5016  94.6294  95.1012  99.6323  99.8336
   year
age 2013    
  0   3.6779
  1  11.3741
  2  22.2070
  3  39.8856
  4  59.4617
  5  99.6322

units:  Tonnes 

Slot "m":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  1 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  2 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  3 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  4 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  5 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  1 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  2 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  3 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  4 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
  5 0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2  0.2 
   year
age 2013
  0 0.2 
  1 0.2 
  2 0.2 
  3 0.2 
  4 0.2 
  5 0.2 

units:  NA 

Slot "mat":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  1 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  2 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
  5 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  1 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  2 0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0  0.0 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
  5 1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0  1.0 
   year
age 2013
  0 0.0 
  1 0.0 
  2 0.0 
  3 0.5 
  4 1.0 
  5 1.0 

units:  NA 

Slot "harvest":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985      1986      1987      1988      1989      1990      1991     
  0 0.0314273 0.0288087 0.0502063 0.0633297 0.0881848 0.0206317 0.0364953
  1 0.1989678 0.1792240 0.3067567 0.4679847 0.2856232 0.4348728 0.3413404
  2 0.3014985 0.4362168 0.4336290 0.6552870 0.6569795 0.8826768 0.8100540
  3 0.2984136 0.2782570 0.3683882 0.5691284 0.8665624 0.6484455 0.8023506
  4 0.2984144 0.2782580 0.3683900 0.5691326 0.8665749 0.6484642 0.8023960
  5 0.2984144 0.2782580 0.3683900 0.5691326 0.8665749 0.6484642 0.8023960
   year
age 1992      1993      1994      1995      1996      1997      1998     
  0 0.0616707 0.0595793 0.0750337 0.0675525 0.0383424 0.0325016 0.0587975
  1 0.3336489 0.3990706 0.3578897 0.4226792 0.3287246 0.3128393 0.4700555
  2 0.9587446 0.8032840 0.9737336 0.6033505 0.5483310 0.7372503 0.6162156
  3 0.6900867 0.5958574 0.7472263 0.6149571 0.5423184 0.6503621 0.4743366
  4 0.6901641 0.5959775 0.7450457 0.6062457 0.5491225 0.7396164 0.5411092
  5 0.6901641 0.5959775 0.7450457 0.6062457 0.5491225 0.7396164 0.5411092
   year
age 1999      2000      2001      2002      2003      2004      2005     
  0 0.0400529 0.0122949 0.0203888 0.0117886 0.0624345 0.0687119 0.0201024
  1 0.3313849 0.3966375 0.3344656 0.4305262 0.3825903 0.4130462 0.3817659
  2 0.6122505 0.6868513 0.8359214 0.7674239 0.9418250 0.6684161 0.7462613
  3 0.5639441 0.6874070 0.7526321 0.4618554 0.7109958 0.6359931 0.5581027
  4 0.6414244 0.7509032 0.6419700 0.3597564 0.6345456 0.7307663 0.6359317
  5 0.6414244 0.7509032 0.6419700 0.3597564 0.6345456 0.7307663 0.6359317
   year
age 2006      2007      2008      2009      2010      2011      2012     
  0 0.0307690 0.0290247 0.0135882 0.0202127 0.0449558 0.1168759 0.0322696
  1 0.3290484 0.4679090 0.5117080 0.3784347 0.3495593 0.3038385 0.2193244
  2 0.7144020 0.6329787 0.6966396 0.6082059 0.5532836 0.5807012 0.4070443
  3 0.5015237 0.5762266 0.5061593 0.4867182 0.7399226 0.6725922 0.3756363
  4 0.5893967 0.5299316 0.3573419 0.5952712 0.8183516 0.5166789 0.3815999
  5 0.5893967 0.5299316 0.3573419 0.5952712 0.8183516 0.5166789 0.3815999
   year
age 2013     
  0 0.0050759
  1 0.2664159
  2 0.5421825
  3 0.4062308
  4 0.3971059
  5 0.3971059

units:  f 

Slot "harvest.spwn":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 2013
  0 0.5 
  1 0.5 
  2 0.5 
  3 0.5 
  4 0.5 
  5 0.5 

units:  prop 

Slot "m.spwn":
An object of class "FLQuant"
, , unit = unique, season = all, area = unique

   year
age 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012
  0 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  1 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  2 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  3 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  4 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
  5 0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5  0.5 
   year
age 2013
  0 0.5 
  1 0.5 
  2 0.5 
  3 0.5 
  4 0.5 
  5 0.5 

units:  NA 

Slot "name":
[1] "Swordfish MED                                      "

Slot "desc":
[1] "Imported from a VPA file. ( /home/laurie/MEGAsync/mse/trade-offs/inputs/swo.idx ).  Sat Mar 28 10:14:36 2015 + FLAssess:  + FLAssess: "

Slot "range":
      min       max plusgroup   minyear   maxyear   minfbar   maxfbar 
        0         5         5      1985      2013         2         4 

Table 4a. XSA diagnostics from continuity run.

FLR XSA Diagnostics 2015-03-28 10:38:53

CPUE data from indices

Catch data for 29 years 1985 to 2013. Ages 0 to 5.

              fleet first age last age first year last year alpha beta
1 Moroccan Longline         2        4       1999      2011  <NA> <NA>
2  Spanish Longline         2        4       1988      2013  <NA> <NA>
3  Scilian Longline         2        4       1991      2009  <NA> <NA>
4   Scilian Gillnet         2        4       1990      2009  <NA> <NA>
5    Greek Longline         2        4       1987      2013  <NA> <NA>
6 Ligurian Longline         2        4       1991      2009  <NA> <NA>


 Time series weights :

    Tapered time weighting applied
   Power =   3 over  20 years

 Catchability analysis :

     Catchability independent of size for ages >   1 

     Catchability independent of age for ages >   4 

 Terminal population estimation :

     Survivor estimates shrunk towards the mean F
    of the final   5 years or the  1 oldest ages.

    S.E. of the mean to which the estimates are shrunk =   0.5 
 
    Minimum standard error for population
    estimates derived from each fleet =  0.3 

    prior weighting not applied

Regression weights
     year
age    2004 2005  2006  2007  2008  2009 2010  2011 2012 2013
  all 0.751 0.82 0.877 0.921 0.954 0.976 0.99 0.997    1    1


 Fishing mortalities
   year
age  2004  2005  2006  2007  2008  2009  2010  2011  2012  2013
  0 0.069 0.020 0.031 0.029 0.014 0.020 0.045 0.117 0.032 0.005
  1 0.413 0.382 0.329 0.468 0.512 0.378 0.350 0.304 0.219 0.266
  2 0.668 0.746 0.714 0.633 0.697 0.608 0.553 0.581 0.407 0.542
  3 0.636 0.558 0.502 0.576 0.506 0.487 0.740 0.673 0.376 0.406
  4 0.731 0.636 0.589 0.530 0.357 0.595 0.818 0.517 0.382 0.397
  5 0.731 0.636 0.589 0.530 0.357 0.595 0.818 0.517 0.382 0.397


 XSA population number (Thousand)
      age
year      0   1   2   3  4  5
  2004 1003 794 391 154 67 66
  2005  788 767 430 164 67 69
  2006  987 633 429 167 77 96
  2007  941 784 373 172 83 75
  2008  785 749 402 162 79 51
  2009  702 634 367 164 80 51
  2010  662 564 355 164 83 56
  2011  873 518 325 167 64 61
  2012  762 636 313 149 70 91
  2013  680 604 418 171 84 86


 Estimated population abundance at 1st Jan  2014 
      age
year   0   1   2   3  4  5
  2014 0 554 379 199 93 46


 Fleet:  Moroccan Longline 

 Log catchability residuals.

   year
age   1999  2000   2001   2002   2003  2004  2005  2006   2007  2008
  2  0.032 0.111 -0.209 -0.103 -0.277 0.008 0.137 0.061  0.119 0.162
  3 -0.038 0.173 -0.247  0.089 -0.149 0.091 0.181 0.073  0.031 0.150
  4 -0.063 0.152 -0.183  0.005 -0.114 0.174 0.329 0.097 -0.048 0.012
   year
age   2009   2010   2011
  2 -0.005 -0.064 -0.073
  3 -0.090 -0.047 -0.207
  4 -0.113 -0.118 -0.103


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -1.5067 -0.6685 0.1209
S.E_Logq   0.1380  0.1380 0.1380


 Fleet:  Spanish Longline 

 Log catchability residuals.

   year
age   1988   1989   1990   1991   1992   1993   1994   1995   1996   1997
  2  0.213 -0.174 -0.254 -0.163 -0.315 -0.070 -0.008 -0.128 -0.399 -0.266
  3 -0.099 -0.019 -0.028 -0.240 -0.243  0.183  0.190  0.126 -0.370 -0.414
  4 -0.589 -0.332  0.296 -0.102 -0.278  0.146  0.371  0.234 -0.059 -0.302
   year
age   1998   1999   2000   2001   2002   2003   2004   2005   2006  2007
  2 -0.204 -0.287 -0.348 -0.300 -0.098 -0.467 -0.482 -0.263 -0.081 0.222
  3 -0.221 -0.346 -0.276 -0.327  0.105 -0.328 -0.388 -0.208 -0.057 0.145
  4 -0.343 -0.363 -0.289 -0.255  0.030 -0.284 -0.296 -0.052 -0.024 0.074
   year
age  2008  2009  2010  2011  2012   2013
  2 0.395 0.134 0.159 0.304 0.370 -0.069
  3 0.393 0.060 0.186 0.181 0.271 -0.061
  4 0.264 0.045 0.124 0.294 0.250 -0.135


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -1.0053 -0.1779 0.6027
S.E_Logq   0.2471  0.2471 0.2471


 Fleet:  Scilian Longline 

 Log catchability residuals.

   year
age   1991  1992 1993   1994  1995 1996   1997   1998  1999   2000  2001
  2 -0.005 0.037   NA -0.074 0.090   NA -0.369  0.163 0.360 -0.180 0.368
  3 -0.105 0.086   NA  0.101 0.321   NA -0.540  0.123 0.278 -0.130 0.318
  4  0.029 0.048   NA  0.278 0.426   NA -0.432 -0.002 0.258 -0.146 0.387
   year
age  2002   2003  2004  2005  2006   2007   2008   2009
  2 0.565 -0.370 0.024 0.065 0.187 -0.259 -0.237 -0.054
  3 0.746 -0.254 0.095 0.097 0.187 -0.359 -0.261 -0.151
  4 0.667 -0.213 0.183 0.250 0.217 -0.433 -0.394 -0.169


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -0.8791 -0.0287 0.7551
S.E_Logq   0.2917  0.2917 0.2917


 Fleet:  Scilian Gillnet 

 Log catchability residuals.

   year
age   1990  1991  1992  1993  1994  1995   1996  1997   1998  1999  2000
  2 -0.264 0.200 0.803 0.470 0.107 0.483 -0.048 0.474  0.159 0.412 0.517
  3 -0.046 0.115 0.867 0.716 0.297 0.729 -0.027 0.318  0.134 0.345 0.582
  4  0.258 0.232 0.812 0.658 0.457 0.817  0.263 0.408 -0.008 0.308 0.549
   year
age  2001 2002 2003  2004  2005  2006 2007   2008   2009
  2 0.499   NA   NA 0.562 0.273 1.197   NA -0.981 -1.442
  3 0.464   NA   NA 0.648 0.320 1.213   NA -0.990 -1.523
  4 0.515   NA   NA 0.718 0.455 1.225   NA -1.140 -1.559


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3       4
Mean_Logq -3.4097 -2.5744 -1.7730
S.E_Logq   0.6459  0.6459  0.6459


 Fleet:  Greek Longline 

 Log catchability residuals.

   year
age   1987   1988 1989   1990  1991   1992  1993  1994   1995 1996 1997
  2 -0.147  0.195   NA -0.147 0.431 -0.421 0.093 0.326 -0.220   NA   NA
  3 -0.650 -0.118   NA  0.079 0.352 -0.349 0.345 0.523  0.033   NA   NA
  4 -1.116 -0.606   NA  0.405 0.493 -0.382 0.310 0.706  0.144   NA   NA
   year
age  1998  1999   2000  2001   2002   2003  2004   2005   2006   2007
  2 0.477 0.231 -0.067 0.098 -0.275 -0.099 0.001 -0.081 -0.034  0.125
  3 0.458 0.170  0.005 0.069 -0.073  0.038 0.094 -0.028 -0.013  0.047
  4 0.339 0.156 -0.005 0.145 -0.145  0.085 0.187  0.131  0.023 -0.021
   year
age   2008   2009  2010   2011   2012  2013
  2  0.014 -0.073 0.109 -0.040 -0.086 0.106
  3  0.011 -0.148 0.135 -0.164 -0.187 0.113
  4 -0.116 -0.160 0.075 -0.048 -0.205 0.042


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.7869 0.0418 0.8198
S.E_Logq   0.2804 0.2804 0.2804


 Fleet:  Ligurian Longline 

 Log catchability residuals.

   year
age   1991   1992   1993   1994   1995   1996   1997   1998   1999   2000
  2 -0.363 -0.595 -0.630 -0.400 -0.414 -0.498 -0.316  0.058 -0.269 -0.046
  3 -0.463 -0.545 -0.399 -0.225 -0.183 -0.491 -0.487  0.018 -0.351  0.004
  4 -0.331 -0.586 -0.442 -0.050 -0.081 -0.186 -0.381 -0.109 -0.373 -0.014
   year
age  2001   2002  2003   2004   2005   2006  2007  2008   2009
  2 0.368 -0.045 0.014 -0.326 -0.589 -0.163 0.594 0.404 -0.067
  3 0.318  0.135 0.130 -0.255 -0.557 -0.162 0.494 0.379 -0.164
  4 0.385  0.055 0.168 -0.169 -0.406 -0.135 0.418 0.244 -0.185


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.6467 0.2038 0.9897
S.E_Logq   0.3144 0.3144 0.3144


 Terminal year survivor and F summaries: 
 
 ,Age 0 Year class =2013 

source 
     scaledWts survivors yrcls
fshk     0.082        60  2013
nshk     0.918       675  2013

 ,Age 1 Year class =2012 

source 
     scaledWts survivors yrcls
fshk         1       273  2012

 ,Age 2 Year class =2011 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.363       186  2011
Greek Longline       0.393       221  2011
fshk                 0.244       187  2011

 ,Age 3 Year class =2010 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.394        88  2010
Greek Longline       0.394       104  2010
fshk                 0.213        63  2010

 ,Age 4 Year class =2009 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.394        40  2009
Greek Longline       0.394        48  2009
fshk                 0.211        45  2009

Table 4b. XSA diagnostics from alternative run.

FLR XSA Diagnostics 2015-03-28 10:38:55

CPUE data from indices

Catch data for 29 years 1985 to 2013. Ages 0 to 5.

              fleet first age last age first year last year alpha beta
1 Moroccan Longline         2        4       1999      2011  <NA> <NA>
2  Spanish Longline         2        4       1988      2013  <NA> <NA>
3  Scilian Longline         2        4       1991      2009  <NA> <NA>
4   Scilian Gillnet         2        4       1990      2009  <NA> <NA>
5    Greek Longline         2        4       1987      2013  <NA> <NA>
6 Ligurian Longline         2        4       1991      2009  <NA> <NA>


 Time series weights :

    Tapered time weighting applied
   Power =   3 over  20 years

 Catchability analysis :

     Catchability independent of size for ages >   1 

     Catchability independent of age for ages >   4 

 Terminal population estimation :

     Survivor estimates shrunk towards the mean F
    of the final   5 years or the  1 oldest ages.

    S.E. of the mean to which the estimates are shrunk =   0.5 
 
    Minimum standard error for population
    estimates derived from each fleet =  0.3 

    prior weighting not applied

Regression weights
     year
age    2004 2005  2006  2007  2008  2009 2010  2011 2012 2013
  all 0.751 0.82 0.877 0.921 0.954 0.976 0.99 0.997    1    1


 Fishing mortalities
   year
age  2004  2005  2006  2007  2008  2009  2010  2011  2012  2013
  0 0.069 0.020 0.031 0.029 0.014 0.020 0.045 0.117 0.032 0.005
  1 0.413 0.382 0.329 0.468 0.512 0.378 0.350 0.304 0.219 0.266
  2 0.668 0.746 0.714 0.633 0.697 0.608 0.553 0.581 0.407 0.542
  3 0.636 0.558 0.502 0.576 0.506 0.487 0.740 0.673 0.376 0.406
  4 0.731 0.636 0.589 0.530 0.357 0.595 0.818 0.517 0.382 0.397
  5 0.731 0.636 0.589 0.530 0.357 0.595 0.818 0.517 0.382 0.397


 XSA population number (Thousand)
      age
year      0   1   2   3  4  5
  2004 1003 794 391 154 67 66
  2005  788 767 430 164 67 69
  2006  987 633 429 167 77 96
  2007  941 784 373 172 83 75
  2008  785 749 402 162 79 51
  2009  702 634 367 164 80 51
  2010  662 564 355 164 83 56
  2011  873 518 325 167 64 61
  2012  762 636 313 149 70 91
  2013  680 604 418 171 84 86


 Estimated population abundance at 1st Jan  2014 
      age
year   0   1   2   3  4  5
  2014 0 554 379 199 93 46


 Fleet:  Moroccan Longline 

 Log catchability residuals.

   year
age   1999  2000   2001   2002   2003  2004  2005  2006   2007  2008
  2  0.032 0.111 -0.209 -0.103 -0.277 0.008 0.137 0.061  0.119 0.162
  3 -0.038 0.173 -0.247  0.089 -0.149 0.091 0.181 0.073  0.031 0.150
  4 -0.063 0.152 -0.183  0.005 -0.114 0.174 0.329 0.097 -0.048 0.012
   year
age   2009   2010   2011
  2 -0.005 -0.064 -0.073
  3 -0.090 -0.047 -0.207
  4 -0.113 -0.118 -0.103


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -1.5067 -0.6685 0.1209
S.E_Logq   0.1380  0.1380 0.1380


 Fleet:  Spanish Longline 

 Log catchability residuals.

   year
age   1988   1989   1990   1991   1992   1993   1994   1995   1996   1997
  2  0.213 -0.174 -0.254 -0.163 -0.315 -0.070 -0.008 -0.128 -0.399 -0.266
  3 -0.099 -0.019 -0.028 -0.240 -0.243  0.183  0.190  0.126 -0.370 -0.414
  4 -0.589 -0.332  0.296 -0.102 -0.278  0.146  0.371  0.234 -0.059 -0.302
   year
age   1998   1999   2000   2001   2002   2003   2004   2005   2006  2007
  2 -0.204 -0.287 -0.348 -0.300 -0.098 -0.467 -0.482 -0.263 -0.081 0.222
  3 -0.221 -0.346 -0.276 -0.327  0.105 -0.328 -0.388 -0.208 -0.057 0.145
  4 -0.343 -0.363 -0.289 -0.255  0.030 -0.284 -0.296 -0.052 -0.024 0.074
   year
age  2008  2009  2010  2011  2012   2013
  2 0.395 0.134 0.159 0.304 0.370 -0.069
  3 0.393 0.060 0.186 0.181 0.271 -0.061
  4 0.264 0.045 0.124 0.294 0.250 -0.135


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -1.0053 -0.1779 0.6027
S.E_Logq   0.2471  0.2471 0.2471


 Fleet:  Scilian Longline 

 Log catchability residuals.

   year
age   1991  1992 1993   1994  1995 1996   1997   1998  1999   2000  2001
  2 -0.005 0.037   NA -0.074 0.090   NA -0.369  0.163 0.360 -0.180 0.368
  3 -0.105 0.086   NA  0.101 0.321   NA -0.540  0.123 0.278 -0.130 0.318
  4  0.029 0.048   NA  0.278 0.426   NA -0.432 -0.002 0.258 -0.146 0.387
   year
age  2002   2003  2004  2005  2006   2007   2008   2009
  2 0.565 -0.370 0.024 0.065 0.187 -0.259 -0.237 -0.054
  3 0.746 -0.254 0.095 0.097 0.187 -0.359 -0.261 -0.151
  4 0.667 -0.213 0.183 0.250 0.217 -0.433 -0.394 -0.169


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3      4
Mean_Logq -0.8791 -0.0287 0.7551
S.E_Logq   0.2917  0.2917 0.2917


 Fleet:  Scilian Gillnet 

 Log catchability residuals.

   year
age   1990  1991  1992  1993  1994  1995   1996  1997   1998  1999  2000
  2 -0.264 0.200 0.803 0.470 0.107 0.483 -0.048 0.474  0.159 0.412 0.517
  3 -0.046 0.115 0.867 0.716 0.297 0.729 -0.027 0.318  0.134 0.345 0.582
  4  0.258 0.232 0.812 0.658 0.457 0.817  0.263 0.408 -0.008 0.308 0.549
   year
age  2001 2002 2003  2004  2005  2006 2007   2008   2009
  2 0.499   NA   NA 0.562 0.273 1.197   NA -0.981 -1.442
  3 0.464   NA   NA 0.648 0.320 1.213   NA -0.990 -1.523
  4 0.515   NA   NA 0.718 0.455 1.225   NA -1.140 -1.559


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2       3       4
Mean_Logq -3.4097 -2.5744 -1.7730
S.E_Logq   0.6459  0.6459  0.6459


 Fleet:  Greek Longline 

 Log catchability residuals.

   year
age   1987   1988 1989   1990  1991   1992  1993  1994   1995 1996 1997
  2 -0.147  0.195   NA -0.147 0.431 -0.421 0.093 0.326 -0.220   NA   NA
  3 -0.650 -0.118   NA  0.079 0.352 -0.349 0.345 0.523  0.033   NA   NA
  4 -1.116 -0.606   NA  0.405 0.493 -0.382 0.310 0.706  0.144   NA   NA
   year
age  1998  1999   2000  2001   2002   2003  2004   2005   2006   2007
  2 0.477 0.231 -0.067 0.098 -0.275 -0.099 0.001 -0.081 -0.034  0.125
  3 0.458 0.170  0.005 0.069 -0.073  0.038 0.094 -0.028 -0.013  0.047
  4 0.339 0.156 -0.005 0.145 -0.145  0.085 0.187  0.131  0.023 -0.021
   year
age   2008   2009  2010   2011   2012  2013
  2  0.014 -0.073 0.109 -0.040 -0.086 0.106
  3  0.011 -0.148 0.135 -0.164 -0.187 0.113
  4 -0.116 -0.160 0.075 -0.048 -0.205 0.042


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.7869 0.0418 0.8198
S.E_Logq   0.2804 0.2804 0.2804


 Fleet:  Ligurian Longline 

 Log catchability residuals.

   year
age   1991   1992   1993   1994   1995   1996   1997   1998   1999   2000
  2 -0.363 -0.595 -0.630 -0.400 -0.414 -0.498 -0.316  0.058 -0.269 -0.046
  3 -0.463 -0.545 -0.399 -0.225 -0.183 -0.491 -0.487  0.018 -0.351  0.004
  4 -0.331 -0.586 -0.442 -0.050 -0.081 -0.186 -0.381 -0.109 -0.373 -0.014
   year
age  2001   2002  2003   2004   2005   2006  2007  2008   2009
  2 0.368 -0.045 0.014 -0.326 -0.589 -0.163 0.594 0.404 -0.067
  3 0.318  0.135 0.130 -0.255 -0.557 -0.162 0.494 0.379 -0.164
  4 0.385  0.055 0.168 -0.169 -0.406 -0.135 0.418 0.244 -0.185


 Mean log catchability and standard error of ages with catchability 
 independent of year class strength and constant w.r.t. time 

                2      3      4
Mean_Logq -0.6467 0.2038 0.9897
S.E_Logq   0.3144 0.3144 0.3144


 Terminal year survivor and F summaries: 
 
 ,Age 0 Year class =2013 

source 
     scaledWts survivors yrcls
fshk     0.082        60  2013
nshk     0.918       675  2013

 ,Age 1 Year class =2012 

source 
     scaledWts survivors yrcls
fshk         1       273  2012

 ,Age 2 Year class =2011 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.363       186  2011
Greek Longline       0.393       221  2011
fshk                 0.244       187  2011

 ,Age 3 Year class =2010 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.394        88  2010
Greek Longline       0.394       104  2010
fshk                 0.213        63  2010

 ,Age 4 Year class =2009 

source 
                 scaledWts survivors yrcls
Spanish Longline     0.394        40  2009
Greek Longline       0.394        48  2009
fshk                 0.211        45  2009